formatting

Author: Rob Patro

README.md

@@ -282,13 +282,15 @@ The `convert` sub-command of `pyroe` can convert the output of `alevin-fry` into
 the native `AnnData` format (`h5ad`).  Further, when performing this conversion, it can organize the unspliced, 
 spliced, and ambiguous counts as desired by the user.
 
-The sub-command takes as input a quantification directory produced by `alevin-fry`, an output structure, 
-an output format, and an output location.  The output structure defines how the `U`, `S`, and `A` layers
-of the input quantification should be represented in the converted matrix.  The syntax for this flag exactly
-mimics the `output_format` argument of the `load_fry` function, which you can read about [here](https://github.com/COMBINE-lab/pyroe#load_fry-notes).  Note that, if you pass in a custom output structure, you should enclose 
-your format description in quotes.  For example, to output to an object where the "main" layer (`X`) contains
-the sum of `U`, `S`, and `A`, and where there is an additional layer named `unspliced` having just the 
-unspliced counts, you would pass `--output-structure '{ "X" : ["U", "S", "A"], "unspliced" : ["U"]}'`. 
+The sub-command takes as input a quantification directory produced by `alevin-fry`, and an output location.
+Additionally, the user should pass in command line parameters to describe the desired output structure, and
+output format. The output structure defines how the `U`, `S`, and `A` layers of the input quantification should
+be represented in the converted matrix.  The syntax for this flag exactly mimics the `output_format` argument of
+the `load_fry` function, which you can read about [here](https://github.com/COMBINE-lab/pyroe#load_fry-notes).
+Note that, if you pass in a custom output structure, you should enclose your format description in quotes.  For
+example, to output to an object where the "main" layer (`X`) contains the sum of `U`, `S`, and `A`, and where
+there is an additional layer named `unspliced` having just the unspliced counts, you would pass
+`--output-structure '{ "X" : ["U", "S", "A"], "unspliced" : ["U"]}'`. 
 
 If you do not explicitly provide an `--output-format`, the default of `h5ad` will be used.